| TUD Organische Chemie | | Immel | | MolArch+ | | Files | | | View or Print (this frame only) |
This list gives an overview on the different files types handled by MolArch+ (list by file extension). For most file types you will find examples in the $MOLARCH/examples directory of the MolArch+ installation. This list is by far not complete yet.
You may also use the non-frames version of this documentation.
*.pdb
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Most common file format for molecular structures (PDB format; Protein Data Base).
HEADER SUCROSE REMARK MOLECULE 1 ATOMS 45 ATOM 1 O5 1 1 -1.033 1.138 0.374 ATOM 2 C1 1 2 -0.602 0.120 1.266 ATOM 3 C2 1 3 -1.804 -0.631 1.845 ... ATOM 45 HO6 1 45 2.346 3.457 -2.807 CONECT 1 2 6 CONECT 2 1 3 12 24 ... CONECT 45 23 ENDMolArch+ recognizes the following PDB records: 'HEADER', 'ATOM', 'HETATM', 'CONECT' 'END', and 'TER'. All other records are ignored and skipped. PDB-files are of fixed column formatted ASCII format. |
*.esp
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ESP-files list atomic charges.
ATOM O XXX XXX XXX 0.000 0.000 0.000-0.260 A ATOM C XXX XXX XXX 0.000 0.000 0.000 0.113 A ATOM C XXX XXX XXX 0.000 0.000 0.000 0.061 A ...These files must match a PDB-file of same base name. The format of ESP-files is fixed column formatted ASCII. |
*.xyz
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XYZ-files list atom types and xyz-coordinates of molecular structures in a free column readable ASCII format. This file type may be used to import non-standard molecular data.
O5 0.084 -.009 -.078 C1 1.503 0.053 -.060 C2 1.977 1.508 -.027 ...The format of XYZ-files is free unformatted ASCII. |
*.hin
|
Hyperchem HIN-files.
forcefield mm+ sys 7.914191 view 40 0.090224 59.65 19.65 ... seed -1109 mol 1 atom 1 - O ** - 0 9.580495 3.285537 -4.517323 2 130 s 273 s atom 2 - C ** - 0 4.48187 1.939143 -1.628475 3 3 a 6 a 42 s atom 3 - C ** - 0 3.651089 0.808005 -1.727865 3 2 a 4 a 37 s ... |
*.mac *.out |
MacroModel OUT- and MAC-files.
151 mtii 1 2 1 3 1 4 1 0 0 0 0 0 0 33.306000 38.974998 21.896999 ... 15 1 1 0 0 0 0 0 0 0 0 0 0 33.679001 38.107002 21.306000 ... 24 1 1 74 1 75 1 0 0 0 0 0 0 33.879002 39.312000 23.261000 ... ... |
*.dg
|
DG-Files obtained from distance geometry calculations.
mtii
151 3 s: 8 o: 8 d: 8
1mtii c1 1 33.223 37.174 18.209 2 3 4 0 0
1mtii o2 2 34.012 36.391 17.814 1 0 0 0 0
1mtii n3 3 31.851 36.878 18.494 1 74 75 0 0
...
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*.dat
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These files list crystal structure data as used by the Cambridge Crystallographic Data Center (CCDC, solid-state structure data base). Structures may be exported from the conquest program using the
FDAT-file format to view and process the data with MolArch+.
#SUCROS1123730820 22 9 0 0 0 2 3 45 0 0 51132200000010000000000073 108648 87028 77578 90102956 90444030151211 0 0 0 0 0 4P21 040 R= .0290 211 0121 0112 0011 0121 6110 0 C 68H 20O 68 C1 29986 35792 48521 C2 10322 13101 54340 C3 31263 47475 63545 ... O9 37733 39888 36855 O10 58164 54571 28597 O11 32654 23865 3981 3 4 5 6 7 8 91011123117 1 6 810 0123739414436 3404245 5 7 9 011 2 2 1 2 3 4 5 6 7 8 11112 435 9431038 |
*.cif *.ins |
Crystal structure data files (ASCII) as used by SHELX and various other crystallographic programs.
... O1A O -0.0845(5) -0.3554(5) 0.11049(18) 0.0712(18) Uani 1 d . . . C1A C -0.0694(7) -0.4451(7) 0.1069(3) 0.065(3) Uani 1 d . . . H1A H -0.1413 -0.5122 0.1076 0.078 Uiso 1 calc R . . ... |
*.ell
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MolArch+ specific file format to save and retrieve atomic thermal anisotropic ellipsoids (ASCII). These files must match a PDB-file of same base name.
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*.sld
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MolArch+ specific file format to save triangulated molecular surfaces and surface qualities (binary data). This file format is also used by other programs such as MOLCAD and Sybyl/Tripos programs.
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*.con
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MolArch+ specific file format to save triangulated molecular surfaces and surface qualities (ASCII).
CONTOUR3D SUCROSE
CONTOURS
DOTS 86
TRIS 165
QUALITIES 1
QUALITY 1 grd (Total Gradients)
ALL DOTS: COOR. X Y Z NORMALS AX AY AZ QUALITIES
1 1 0.38340E+01 0.12670E+01-0.24550E+01 0.30075E-01 0.69017E-01 0.99716E+00 0.29758E+03
...
86 2 0.38340E+01-0.14200E+01-0.24550E+01 0.33383E-01-0.54168E-01 0.99797E+00 0.32840E+03
ALL TRIS: NUMBER OF DOTS
1 2 47 46 50
2 2 50 45 66
...
165 2 61 57 60
|
*.cub
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GAUSSIAN cube grid data files that may be read and imported by MolArch+.
Salicylsaeure, spez. Position
SCF Molecular Orbitals
-16 -11.417476 -9.298097 -6.513076
98 0.217205 0.000000 0.000000
86 0.000000 0.217205 0.000000
61 0.000000 0.000000 0.217205
6 6.000000 0.384791 -0.462750 0.000050
6 6.000000 -0.969903 1.854038 0.000007
6 6.000000 -3.624020 1.810000 -0.000257
...
2 37 36
-6.30261E-05 -2.19944E-05 -6.88207E-05 -2.40159E-05 -7.47492E-05 -2.60839E-05
-8.07505E-05 -2.81771E-05 -8.67548E-05 -3.02711E-05 -9.26838E-05 -3.23386E-05
...
|
*.CON
|
MolArch+ specific file format to save grid data (ASCII).
SCF Molecular Orbitals
98 86 61
0.114940E+00 0.114940E+00 0.114940E+00
-0.604187E+01 -0.492034E+01 -0.344657E+01
0.000000E+00 0.000000E+00
-0.219944E-04
-0.255131E-04
...
LINE 1 (FORMAT 'A'): Title
LINE 2 (FORMAT '3I14'): STEPS IN X-, Y-, AND Z-DIRECTION
LINE 3 (FORMAT '3E14.6'): STEP SIZE IN X-, Y-, AND Z-DIRECTION
LINE 4 (FORMAT '3E14.6'): START OF X-, Y-, AND Z-AXIS
LINE 5 (FORMAT '2E14.6'): DATA MINIMUM AND MAXIMUM (MAY BE 0.0, 0.0)
LINE 6 (FORMAT '3E14.6'): DATA (X-INDEX RUNNING FASTEST, Z-INDEX SLOWEST)
...
|
*.ein *.opt *.log |
Files (ASCII) used and generated by the force-field program PIMM which are also handled by MolArch+.
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*.log
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GAUSSIAN output (LOG) files (ASCII) which may be used by MolArch+ to import molecular structures and atomic charges.
...
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 0.000000 1.396579 0.000000
2 6 0 -1.209474 0.698396 0.000000
3 6 0 -1.209488 -0.698267 0.000000
...
10 1 0 -0.000021 -2.483602 0.000000
11 1 0 2.150831 -1.241961 0.000000
12 1 0 2.150886 1.241758 0.000000
---------------------------------------------------------------------
...
|
*.spr
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Script parameter files that may contain sequences of MolArch+ commands to be executed.
pdbload ribbon01.pdb reset molecules delete single-atoms hydrogens single-bonds molecule 2 RELABEL CPK molecule 2 ... |
*.com
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Shell scripts that may use MolArch+ and other shell command sequences (particularly useful for creating molecular animations).
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*.par
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MolArch+ specific file format for saving parameter files which describe molecular fragments and connectivities (without atomic coordinates).
FRAGMENT SEARCH: SINGLE PYRANOSE UNIT SIZE MIN SPC 22 22 0 SORT NO BONDS BONDED ATOMS C1 1 0 C2 2 1 1 C3 3 1 2 C4 4 1 3 ... |
